KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-GFP	Abcam	Cat# ab290, RRID:AB_303395
Rabbit anti-TIS11B	Cell Signaling	Cat# 30894
Mouse anti-GAPDH	Sigma-Aldrich	Cat# G8795, RRID:AB_1078991
Rabbit anti-Calnexin	Abcam	Cat# ab22595, RRID:AB_2069006
Rabbit anti-H3	Cell Signaling	Cat# 9715, RRID:AB_331563
Chicken anti-GFP	Abcam	Cat# Ab13970, RRID:AB_300798
Donkey anti-mouse IRDye 700	Rockland	Cat# 610-730-002, RRID:AB_1660934
Donkey anti-rabbit IRDye 800	LI-COR Biosciences	Cat# 926-32213, RRID:AB_621848
Donkey anti-mouse IRDye 800	LI-COR Biosciences	Cat# 926-32212, RRID:AB_621847
Chemicals, peptides, and recombinant proteins
Stellaris® FISH Probes, eGFP with Quasar® 670 Dye	Biosearchtech	Cat# VSMF-1015-5
Lipofectamine 3000	ThermoFisher	Cat# L3000001
Chloroquine diphosphate salt	Millipore-Sigma	Cat# 6628
Fibronectin	Millipore-Sigma	Cat# F0635
Odyssey blocking buffer (PBS)	LI-COR Biosciences	Cat# 927-40000
SeeBlue Plus2 Pre-Stained Standard	Thermo Fisher Scientific	Cat# LC5925
NuPAGE MES SDS running buffer 20x	Invitrogen	Cat# NP0002
NuPAGE Novex 4-12% Bis-Tris Protein Gels, 1.0 mm, 10 well	Invitrogen	Cat# NP0321
NuPAGE Transfer Buffer	Invitrogen	Cat# NP00061
Sample Buffer, Laemmli 2× Concentrate	Sigma-Aldrich	Cat# S3401
Tween-20	Fisher Scientific	Cat# BP337-500
Triton X-100	Fisher Scientific	Cat# BP151-100
Nonidet P-40	Sigma-Aldrich	Cat# 74385
IGEPAL CA-630	Millipore-Sigma	Cat# I8896
Doxycycline Hydrochloride	Millipore-Sigma	Cat# D3447
Ampicillin Sodium Salt	Fisher Scientific	Cat# BP176025
Puromycin Dihydrochloride	Fisher Scientific	Cat# A1113803
Bovine Serum Albumin (BSA)	Fisher Scientific	Cat# BP1605100
Tris Base	Fisher Scientific	Cat# BP152-1
Sodium Chloride	Fisher Scientific	Cat# S271-3
Dextran Sulfate Sodium Salt	Spectrum Chemical	Cat# DE131
Dextran Sulfate 50% solution	Millipore-Sigma	Cat# S4030
Ethylene Carbonate, 98%	Millipore-Sigma	Cat# E26258-500G
Ribonucleoside Vanadyl Complex	NEB	Cat# S1402
Salmon testes single stranded DNA	Sigma-Aldrich	Cat# D7656
Yeast tRNA	Life Technologies	Cat# 15401029
Formamide	Sigma-Aldrich	Cat# F7503
Murine RNase Inhibitor	NEB	Cat# M0314S
AMPure XP	Fisher Scientific	Cat# NC9959336
Protein A/G Magnetic Beads	ThermoFisher	Cat# 88802
Superscript IV Reverse Transcriptase	ThermoFisher	Cat# 18090010
DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride)	Life Technologies	Cat# D1306
Quant-it Ribogreen RNA Reagent	ThermoFisher	Cat# R11491
TRI Reagent™ Solution	Invitrogen	Cat# AM9738
SuperScript IV VILO Master Mix with ezDNase	Invitrogen	Cat# 11766050
Q5 High-Fidelity DNA Polymerase	NEB	Cat# M0491L
T4 DNA Ligase	NEB	Cat# M0202L
DNA Polymerase I, Large (Klenow) Fragment	NEB	Cat# M0210L
UltraPure agarose	Invitrogen	Cat# 16500500
Ethidium Bromide	Fisher Scientific	Cat# PI17898
16% Paraformaldehde Aqueous Solution	Fisher Scientific	Cat# 50-980-487
ProLong Gold Antifade Mountant	ThermoFisher	Cat# P36934
ProLong Diamond Antifade Mountant	ThermoFisher	Cat# P36961
Methanol	Fisher Scientific	Cat# A412-4
Ethanol	Fisher Scientific	Cat# BP28184
Isopropanol	Fisher Scientific	Cat# BP26184
Chloroform	Fisher Scientific	Cat# C607-4
Urea	Sigma Aldrich	Cat# U0631
EPPS	Sigma Aldrich	Cat# E9502-1KG
cOmplete EDTA-free Protease Inhibitor Cocktail	Roche	Cat# 04-693-159-001
Phosphatase Inhibitor Cocktail 2	Sigma Aldrich	Cat# P5726
Phosphatase Inhibitor Cocktail 3	Sigma Aldrich	Cat# P0044
Benzonase	Sigma Aldrich	Cat# E8263-5KU
TCEP Solution	ThermoFisher	Cat# PI77720
Lysyl endopeptidase	FUJIFILM Wako	Cat# 129-02541
Sequencing Grade Modified Trypsin	Promega	Cat# V5111
Acetonitrile anhydrous	Sigma Aldrich	Cat# 271004
Hydroxylamine	Sigma Aldrich	Cat# 467804
Trifluoroacetic acid	Sigma Aldrich	Cat# T6508-10AMP
Ammonium biocarbonate BioUltra	Sigma Aldrich	Cat# 09830
Water, Optima LC/MS Grade	FisherScientific	Cat# W6-1
Formic acid	FisherScientific	Cat# A117-10X1AMP
Critical commercial assays
QIAGEN Plasmid Plus Midi Kit	Qiagen	Cat# 12945
TMTpro 16plex Label Reagent Set	ThermoFisher	Cat# A44520
Experimental models: Cell lines
HeLa	Jonathan S. Weissman	N/A
HEK293T	ATCC	ATCC Cat# CRL-3216, RRID:CVCL_0063
Oligonucleotides	This paper	Table S6
Recombinant DNA
pcDNA-GFP-TIS11B	Ma and Mayr16	N/A
pcDNA-BFP-TIS11B	Ma and Mayr16	N/A
pcDNA-mCherry-TIS11B	Ma and Mayr16	N/A
pcDNA-GFP-SEC61B	Ma and Mayr16	N/A
pcDNA-BFP-SEC61B	Ma and Mayr16	N/A
pcDNA-mCherry-SEC61B	Ma and Mayr16	N/A
pcDNA-GFP	Ma and Mayr16	N/A
pcDNA-mCherry	Ma and Mayr16	N/A
pcDNA-BIRC3-MS2-SU	Lee and Mayr39	N/A
pFRT_TO_FlagHA_TIAL1	Meyer et al.36	Addgene106090
UBC NLS-HA-2XMCP-tagRFPt	Halstead et al.52	Addgene 64541
pHR-tdPP7-3xmCherry	Yan et al.32	Addgene 74926
pHR-scFv-GCN4-sfGFP-GB1-dWPRE	Yan et al.32	Addgene 60907
pcDNA4TO-24xGCN4_v4-kif18b-24xPP7	Yan et al.32	Addgene 74928
pcDNA-GFP-THAP1-MS2	This paper	N/A
pcDNA-MCP-mCherry	This paper	N/A
pcDNA-MCP-mCherry-TIS11B	This paper	N/A
pcDNA-MCP-mCherry-HuR	Lee and Mayr39	N/A
pcDNA-MCP-mCherry-TIAL1	This paper	N/A
pcDNA-MCP-mCherry-SEC61B	This paper	N/A
pcDNA-TRAPa-MCP-mCherry	This paper	N/A
pcDNA-MCP-mCherry-CAAX	This paper	N/A
pcDNA-MCP-mCherry-TIAL1-CAAX	This paper	N/A
pcDNA-TIS11B-MCP-mCherry-SEC61B	This paper	N/A
Software and algorithms
FIJI	NIH	https://fiji.sc/
MATLAB	MATLAB	https://www.mathworks.com/products/matlab.html
HOMER	UCSD	http://homer.ucsd.edu/homer/
GraphPad Prism 8	GraphPad Software	https://www.graphpad.com/scientific-software/prism
FlowJo_V10	FlowJo	https://www.fiowjo.com
SPSS Software Version 14	IBM SPSS Statistics	https://www.ibm.com/products/spss-statistics
R Studio	R Project	https://www.r-project.org/
Odyssey	LI-COR Biosciences	https://www.licor.com/bio/products/imaging_systems/odyssey/
Deposited data
Raw data	This paper	https://doi.org/10.17632/nmt7ppsp8r1
Image analysis scripts	This paper	https://doi.org/10.17632/nmt7ppsp8r1
RNA-seq datasets	This paper	GEO, Accession number: GSE215770
Proteomics dataset	This paper	MassIVE repository (sitory (dataset identifier MSV000092176)
Original code for data analysis	This paper	https://doi.org/10.5281/zenodo.10056230